
# Create a temporary directory to hold notebook output, and change the working directory to that directory.
from tempfile import TemporaryDirectory
import os
import shutil
data_dir = TemporaryDirectory()

os.chdir(data_dir.name)


import os
if 'CRDS_CACHE_TYPE' in os.environ:
    if os.environ['CRDS_CACHE_TYPE'] == 'local':
        os.environ['CRDS_PATH'] = os.path.join(os.environ['HOME'], 'crds', 'cache')
    elif os.path.isdir(os.environ['CRDS_CACHE_TYPE']):
        os.environ['CRDS_PATH'] = os.environ['CRDS_CACHE_TYPE']
print('CRDS cache location: {}'.format(os.environ['CRDS_PATH']))

CRDS cache location: /grp/crds/cache


import warnings
import psutil
from astropy.io import fits

# Only print a DeprecationWarning the first time it shows up, not every time.
with warnings.catch_warnings():
    warnings.simplefilter("once", category=DeprecationWarning)
    import jwst
    from jwst.pipeline.calwebb_detector1 import Detector1Pipeline
    from jwst.assign_wcs.assign_wcs_step import AssignWcsStep
    from jwst.msaflagopen.msaflagopen_step import MSAFlagOpenStep
    from jwst import datamodels

# The latest version of NPTT is installed in the requirements text file at:
# /jwst_validation_notebooks/environment.yml

# import NPTT
import nirspec_pipe_testing_tool as nptt

# To get data from Artifactory
from ci_watson.artifactory_helpers import get_bigdata


# Make sure that the version used is the right one

pipeline_version = jwst.__version__
nptt_version = nptt.__version__

print("Using jwst pipeline version: ", pipeline_version)
print("Using NPTT version: ", nptt_version)

Using jwst pipeline version:  1.8.2
Using NPTT version:  2.0.1


testing_data = {                
                'mos_prism_clear':{
                                  'uncal_file_nrs1': 'mos_prism_nrs1_uncal.fits',
                                  'uncal_file_nrs2': 'mos_prism_nrs2_uncal.fits',
                                  'msa_shutter_config': 'V0030006000104_msa.fits' },
                
                'mos_g140m_f100lp':{
                                  'uncal_file_nrs1': 'mos_g140m_line1_NRS1_uncal.fits',
                                  'uncal_file_nrs2': 'mos_g140m_line1_NRS2_uncal.fits',  
                                  'msa_shutter_config': 'V8460001000101_msa.fits' },
                
                'ifu_prism_clear':{
                                  'uncal_file_nrs1': 'ifu_prism_nrs1_uncal.fits',
                                  'uncal_file_nrs2': 'ifu_prism_nrs2_uncal.fits',
                                  'msa_shutter_config': None },

                'ifu_g395h_f290lp':{
                                  'uncal_file_nrs1': 'ifu_g395h_f290lp_nrs1_uncal.fits',
                                  'uncal_file_nrs2': 'ifu_g395h_f290lp_nrs2_uncal.fits',
                                  'msa_shutter_config': None }

               }


# define function to pull data from Artifactory
def get_artifactory_file(data_set_dict, detector):
    """This function creates a list with all the files needed per detector to run the test.
    Args:
        data_set_dict: dictionary, contains inputs for a specific mode and configuration
        detector: string, either nrs1 or nrs2
    Returns:
        data: list, contains all files needed to run test
    """
    files2obtain = ['uncal_file_nrs1', 'msa_shutter_config']
    data = []
    for file in files2obtain:
        data_file = None
        try: 
            if '_nrs' in file and '2' in detector:
                file = file.replace('_nrs1', '_nrs2')

            data_file = get_bigdata('jwst_validation_notebooks',
                                         'validation_data',
                                         'nirspec_data', 
                                         data_set_dict[file])
        except TypeError:
            data.append(None)
            continue

        data.append(data_file)

    return data


# Set common NPTT switches for this test

# accepted threshold difference with respect to benchmark files
msa_flagging_threshold = 99.5

# other NPTT variables
stellarity = None
operability_ref = None
source_type = None
save_figs = False
show_figs = True
debug = False
verbose = False

# Get the data
results_dict = {}
detectors = ['nrs1', 'nrs2']
for mode_config, data_set_dict in testing_data.items():
    for det in detectors:
        print('Testing files for detector: ', det)
        data = get_artifactory_file(data_set_dict, det)
        uncal_file, msa_shutter_config = data
        print('Working with uncal_file: ', uncal_file)
        uncal_basename = os.path.basename(uncal_file)
                
        # Run the stage 1 pipeline 
        rate_object = Detector1Pipeline.call(uncal_file)
        # Make sure the MSA shutter configuration file is set up correctly
        if msa_shutter_config is not None:
            msa_metadata = rate_object.meta.instrument.msa_metadata_file
            print(msa_metadata)
            if msa_metadata is None or msa_metadata == 'N/A':
                rate_object.meta.instrument.msa_metadata_file = msa_shutter_config

        # Run the stage 2 pipeline steps
        try:
            pipe_object = AssignWcsStep.call(rate_object)
            skip_file = False
        except:
            print("An error occured with AssignWcs. Likely: No open slits fall on detector", det)
            print("Skipping test for this file. \n")
            skip_file = True
       
        if not skip_file:
            msa_flagging_object = MSAFlagOpenStep.call(pipe_object)

            # Run the validation test
            %matplotlib inline

            result, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.msa_flagging_testing.run_msa_flagging_testing(
                                                                        msa_flagging_object, 
                                                                        msa_flagging_threshold = msa_flagging_threshold,
                                                                        rate_obj = rate_object,
                                                                        stellarity = stellarity, 
                                                                        operability_ref = operability_ref, 
                                                                        save_figs = save_figs, 
                                                                        show_figs = show_figs, 
                                                                        source_type = source_type, 
                                                                        debug = debug)

        else:
            result = 'skipped'


        # Did the test pass
        print("Did msa_flagging validation test pass? ", result, "\n\n")
        rd = {uncal_basename: result}
        results_dict.update(rd)
        
        # close all open files
        psutil.Process().open_files()
        closing_files = []
        for fd in psutil.Process().open_files():
            if data_dir.name in fd.path:
                closing_files.append(fd)
        for fd in closing_files:
            try:
                if verbose:
                    print('Closing file: ', fd)
                open(fd.fd).close()
            except:
                if verbose:
                    print('File already closed: ', fd)

Testing files for detector:  nrs1
Working with uncal_file:  /internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpxni5gg5y/mos_prism_nrs1_uncal.fits

2022-12-03 23:52:23,634 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2022-12-03 23:52:23,662 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2022-12-03 23:52:23,664 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2022-12-03 23:52:23,665 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2022-12-03 23:52:23,666 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2022-12-03 23:52:23,667 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2022-12-03 23:52:23,669 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2022-12-03 23:52:23,670 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2022-12-03 23:52:23,671 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2022-12-03 23:52:23,672 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2022-12-03 23:52:23,673 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2022-12-03 23:52:23,674 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2022-12-03 23:52:23,675 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2022-12-03 23:52:23,676 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2022-12-03 23:52:23,678 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2022-12-03 23:52:23,679 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2022-12-03 23:52:23,680 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2022-12-03 23:52:23,682 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2022-12-03 23:52:23,894 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpxni5gg5y/mos_prism_nrs1_uncal.fits',).
2022-12-03 23:52:23,904 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'n_pix_grow_sat': 1}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0, 'after_jump_flag_dn1': 0.0, 'after_jump_flag_time1': 0.0, 'after_jump_flag_dn2': 0.0, 'after_jump_flag_time2': 0.0, 'min_sat_area': 1.0, 'min_jump_area': 5.0, 'expand_factor': 2.0, 'use_ellipses': False, 'sat_required_snowball': True, 'expand_large_events': False}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'suppress_one_group': True, 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2022-12-03 23:52:24,090 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'mos_prism_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2022-12-03 23:52:24,102 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0086.fits'.
2022-12-03 23:52:24,105 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits'.
2022-12-03 23:52:24,107 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits'.
2022-12-03 23:52:24,109 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits'.
2022-12-03 23:52:24,111 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2022-12-03 23:52:24,111 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits'.
2022-12-03 23:52:24,113 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_refpix_0022.fits'.
2022-12-03 23:52:24,117 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2022-12-03 23:52:24,117 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2022-12-03 23:52:24,117 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits'.
2022-12-03 23:52:24,120 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0113.fits'.
2022-12-03 23:52:24,122 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2022-12-03 23:52:24,122 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2022-12-03 23:52:24,123 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2022-12-03 23:52:24,576 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2022-12-03 23:52:24,577 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpxni5gg5y'}
2022-12-03 23:52:24,718 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2022-12-03 23:52:24,719 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2022-12-03 23:52:24,722 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2022-12-03 23:52:24,919 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2022-12-03 23:52:24,922 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpxni5gg5y'}
2022-12-03 23:52:24,945 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits
2022-12-03 23:52:26,033 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2022-12-03 23:52:26,233 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2022-12-03 23:52:26,235 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpxni5gg5y', 'n_pix_grow_sat': 1}
2022-12-03 23:52:26,259 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits
2022-12-03 23:52:28,371 - stpipe.Detector1Pipeline.saturation - INFO - Detected 49730 saturated pixels
2022-12-03 23:52:28,405 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2022-12-03 23:52:28,432 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2022-12-03 23:52:28,608 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2022-12-03 23:52:28,610 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpxni5gg5y'}
2022-12-03 23:52:28,611 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2022-12-03 23:52:28,614 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2022-12-03 23:52:28,764 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2022-12-03 23:52:28,766 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpxni5gg5y'}
2022-12-03 23:52:28,797 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0113.fits
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stdatamodels/validate.py:38: ValidationWarning: While validating meta.exposure.readpatt the following error occurred:
'ALLIRS2' is not one of ['ACQ1', 'ACQ2', 'BRIGHT1', 'BRIGHT2', 'DEEP2', 'DEEP8', 'FAST', 'FASTGRPAVG', 'FASTGRPAVG8', 'FASTGRPAVG16', 'FASTGRPAVG32', 'FASTGRPAVG64', 'FASTR1', 'FASTR100', 'FGS', 'FGS60', 'FGS8370', 'FGS840', 'FGSRAPID', 'FINEGUIDE', 'ID', 'MEDIUM2', 'MEDIUM8', 'NIS', 'NISRAPID', 'NRS', 'NRSIRS2', 'NRSN16R4', 'NRSN32R8', 'NRSN8R2', 'NRSRAPID', 'NRSIRS2RAPID', 'NRSRAPIDD1', 'NRSRAPIDD2', 'NRSRAPIDD6', 'NRSSLOW', 'RAPID', 'SHALLOW2', 'SHALLOW4', 'SLOW', 'SLOWR1', 'TRACK', 'ANY', 'N/A']

Failed validating 'enum' in schema:
    OrderedDict([('title', 'Readout pattern'),
                 ('type', 'string'),
                 ('enum',
                  ['ACQ1',
                   'ACQ2',
                   'BRIGHT1',
                   'BRIGHT2',
                   'DEEP2',
                   'DEEP8',
                   'FAST',
                   'FASTGRPAVG',
                   'FASTGRPAVG8',
                   'FASTGRPAVG16',
                   'FASTGRPAVG32',
                   'FASTGRPAVG64',
                   'FASTR1',
                   'FASTR100',
                   'FGS',
                   'FGS60',
                   'FGS8370',
                   'FGS840',
                   'FGSRAPID',
                   'FINEGUIDE',
                   'ID',
                   'MEDIUM2',
                   'MEDIUM8',
                   'NIS',
                   'NISRAPID',
                   'NRS',
                   'NRSIRS2',
                   'NRSN16R4',
                   'NRSN32R8',
                   'NRSN8R2',
                   'NRSRAPID',
                   'NRSIRS2RAPID',
                   'NRSRAPIDD1',
                   'NRSRAPIDD2',
                   'NRSRAPIDD6',
                   'NRSSLOW',
                   'RAPID',
                   'SHALLOW2',
                   'SHALLOW4',
                   'SLOW',
                   'SLOWR1',
                   'TRACK',
                   'ANY',
                   'N/A']),
                 ('fits_ke ...
  warnings.warn(errmsg, ValidationWarning)
2022-12-03 23:52:34,630 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2022-12-03 23:52:34,873 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2022-12-03 23:52:34,876 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpxni5gg5y', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2022-12-03 23:52:34,909 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /grp/crds/cache/references/jwst/jwst_nirspec_refpix_0022.fits
2022-12-03 23:52:38,832 - stpipe.Detector1Pipeline.refpix - INFO - Working on integration 1
2022-12-03 23:52:53,395 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2022-12-03 23:52:53,717 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2022-12-03 23:52:53,720 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpxni5gg5y'}
2022-12-03 23:52:53,748 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits
2022-12-03 23:52:58,545 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2022-12-03 23:52:58,681 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2022-12-03 23:52:58,683 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpxni5gg5y', 'dark_output': None}
2022-12-03 23:52:58,768 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0086.fits
2022-12-03 23:53:41,597 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=4, nframes=1, groupgap=0
2022-12-03 23:53:41,599 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=65, nframes=1, groupgap=0
2022-12-03 23:53:42,189 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2022-12-03 23:53:42,365 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2022-12-03 23:53:42,367 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpxni5gg5y', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0, 'after_jump_flag_dn1': 0.0, 'after_jump_flag_time1': 0.0, 'after_jump_flag_dn2': 0.0, 'after_jump_flag_time2': 0.0, 'min_sat_area': 1.0, 'min_jump_area': 5.0, 'expand_factor': 2.0, 'use_ellipses': False, 'sat_required_snowball': True, 'expand_large_events': False}
2022-12-03 23:53:42,406 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2022-12-03 23:53:42,451 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2022-12-03 23:53:42,555 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2022-12-03 23:53:44,180 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2022-12-03 23:53:44,224 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/twopoint_difference.py:154: RuntimeWarning: All-NaN slice encountered
  max_ratio = np.nanmax(ratio, axis=0)
2022-12-03 23:53:45,682 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier, two-point found 0 pixels with at least one CR from five or more groups.
2022-12-03 23:53:46,312 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 2.13119 sec
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/jump.py:302: RuntimeWarning: invalid value encountered in divide
  data /= gain_2d
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/jump.py:303: RuntimeWarning: invalid value encountered in divide
  err /= gain_2d
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/jump.py:304: RuntimeWarning: invalid value encountered in divide
  readnoise_2d /= gain_2d
2022-12-03 23:53:46,367 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 3.960269
2022-12-03 23:53:46,373 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2022-12-03 23:53:46,527 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 4, 3200, 2048) from mos_prism_nrs1_uncal.fits>,).
2022-12-03 23:53:46,529 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpxni5gg5y', 'int_name': '', 'save_opt': False, 'opt_name': '', 'suppress_one_group': True, 'maximum_cores': 'none'}
2022-12-03 23:53:46,626 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2022-12-03 23:53:46,627 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2022-12-03 23:53:46,750 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2022-12-03 23:53:46,751 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/ramp_fitting/ols_fit.py:1089: RuntimeWarning: invalid value encountered in multiply
  var_p4[num_int, :, :, :] *= (segs_4[num_int, :, :, :] > 0)
2022-12-03 23:54:01,164 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 4
2022-12-03 23:54:01,165 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2022-12-03 23:54:01,352 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2022-12-03 23:54:01,510 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from mos_prism_nrs1_uncal.fits>,).
2022-12-03 23:54:01,512 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpxni5gg5y'}
2022-12-03 23:54:01,591 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2022-12-03 23:54:01,592 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2022-12-03 23:54:01,597 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2022-12-03 23:54:01,712 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from mos_prism_nrs1_uncal.fits>,).
2022-12-03 23:54:01,714 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpxni5gg5y'}
2022-12-03 23:54:01,788 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2022-12-03 23:54:01,789 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2022-12-03 23:54:01,794 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2022-12-03 23:54:01,795 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2022-12-03 23:54:01,795 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-03 23:54:01,795 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2022-12-03 23:54:01,806 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2022-12-03 23:54:01,924 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from mos_prism_nrs1_uncal.fits>,).
2022-12-03 23:54:01,925 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.1, 'sip_degree': None, 'sip_max_inv_pix_error': 0.1, 'sip_inv_degree': None, 'sip_npoints': 12, 'slit_y_low': -0.55, 'slit_y_high': 0.55}

N/A

2022-12-03 23:54:02,083 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2022-12-03 23:54:02,129 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2022-12-03 23:54:02,130 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2022-12-03 23:54:02,131 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2022-12-03 23:54:02,133 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2022-12-03 23:54:02,413 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS1: [3, 4]
2022-12-03 23:54:02,414 - stpipe.AssignWcsStep - INFO - Computing WCS for 2 open slitlets
2022-12-03 23:54:02,454 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2022-12-03 23:54:02,455 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2022-12-03 23:54:02,455 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2022-12-03 23:54:02,457 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2022-12-03 23:54:02,472 - stpipe.AssignWcsStep - INFO - SPORDER= 0, wrange=[6e-07, 5.3e-06]
2022-12-03 23:54:02,626 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 1
2022-12-03 23:54:02,627 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 2
2022-12-03 23:54:02,627 - stpipe.AssignWcsStep - INFO - There are 1 open slits in quadrant 3
2022-12-03 23:54:02,636 - stpipe.AssignWcsStep - INFO - There are 1 open slits in quadrant 4
2022-12-03 23:54:02,646 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 5
2022-12-03 23:54:02,824 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0034.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0028.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpxni5gg5y/V0030006000104_msa.fits'}
2022-12-03 23:54:03,018 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2022-12-03 23:54:03,032 - stpipe.AssignWcsStep - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-03 23:54:03,032 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2022-12-03 23:54:03,042 - stpipe.MSAFlagOpenStep - INFO - MSAFlagOpenStep instance created.
2022-12-03 23:54:03,178 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep running with args (<ImageModel(2048, 2048) from mos_prism_nrs1_uncal.fits>,).
2022-12-03 23:54:03,179 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2022-12-03 23:54:03,197 - stpipe.MSAFlagOpenStep - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2022-12-03 23:54:03,198 - stpipe.JwstStep - INFO - JwstStep instance created.
2022-12-03 23:54:03,323 - stpipe.MSAFlagOpenStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2022-12-03 23:54:03,324 - stpipe.MSAFlagOpenStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2022-12-03 23:54:03,325 - stpipe.MSAFlagOpenStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2022-12-03 23:54:03,326 - stpipe.MSAFlagOpenStep - INFO - theta_x correction: 0.0 deg
2022-12-03 23:54:03,340 - stpipe.MSAFlagOpenStep - INFO - SPORDER= 0, wrange=[6e-07, 5.3e-06]
2022-12-03 23:54:03,490 - stpipe.MSAFlagOpenStep - INFO - There are 5 open slits in quadrant 1
2022-12-03 23:54:03,528 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 2
2022-12-03 23:54:03,552 - stpipe.MSAFlagOpenStep - INFO - There are 9 open slits in quadrant 3
2022-12-03 23:54:03,621 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 4
2022-12-03 23:54:03,645 - stpipe.MSAFlagOpenStep - INFO - There are 0 open slits in quadrant 5
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2588.086193887466.
  warnings.warn(f"Invalid interval: upper bound {upper} "
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2332.7637849323596.
  warnings.warn(f"Invalid interval: upper bound {upper} "
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2734.225436305883.
  warnings.warn(f"Invalid interval: upper bound {upper} "
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2098.587600763162.
  warnings.warn(f"Invalid interval: upper bound {upper} "
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2088.836558573466.
  warnings.warn(f"Invalid interval: upper bound {upper} "
2022-12-03 23:54:16,565 - stpipe.MSAFlagOpenStep - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-03 23:54:16,566 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep done

2022-12-03 23:54:17,382 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2022-12-03 23:54:17,393 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2022-12-03 23:54:17,646 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from mos_prism_nrs1_uncal.fits>,).
2022-12-03 23:54:17,648 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.1, 'sip_degree': None, 'sip_max_inv_pix_error': 0.1, 'sip_inv_degree': None, 'sip_npoints': 12, 'slit_y_low': -0.45, 'slit_y_high': 0.45}
2022-12-03 23:54:17,794 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2022-12-03 23:54:17,855 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2022-12-03 23:54:17,856 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2022-12-03 23:54:17,857 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2022-12-03 23:54:17,859 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2022-12-03 23:54:18,073 - stpipe.AssignWcsStep - INFO - Removing slit 1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 23:54:18,112 - stpipe.AssignWcsStep - INFO - Removing slit 2 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 23:54:18,294 - stpipe.AssignWcsStep - INFO - Removing slit 6 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 23:54:18,339 - stpipe.AssignWcsStep - INFO - Removing slit 7 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 23:54:18,385 - stpipe.AssignWcsStep - INFO - Removing slit 8 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 23:54:18,928 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS1: [3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
2022-12-03 23:54:18,930 - stpipe.AssignWcsStep - INFO - Computing WCS for 14 open slitlets
2022-12-03 23:54:18,967 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.0332140289247036 deg
2022-12-03 23:54:18,969 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3367482721805573 deg
2022-12-03 23:54:18,969 - stpipe.AssignWcsStep - INFO - theta_y correction: -1.0907214098475986e-05 deg
2022-12-03 23:54:18,971 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2022-12-03 23:54:18,987 - stpipe.AssignWcsStep - INFO - SPORDER= 0, wrange=[6e-07, 5.3e-06]
2022-12-03 23:54:19,150 - stpipe.AssignWcsStep - INFO - There are 3 open slits in quadrant 1
2022-12-03 23:54:19,175 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 2
2022-12-03 23:54:19,177 - stpipe.AssignWcsStep - INFO - There are 9 open slits in quadrant 3
2022-12-03 23:54:19,244 - stpipe.AssignWcsStep - INFO - There are 2 open slits in quadrant 4
2022-12-03 23:54:19,261 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 5
2022-12-03 23:54:19,414 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0034.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0028.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': 'fopens_metafile_msa.fits'}
2022-12-03 23:54:20,057 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2022-12-03 23:54:20,073 - stpipe.AssignWcsStep - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-03 23:54:20,073 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done

Working with slit/slice:  3
Slit min and max in y direction:  -0.5 0.5
bounding box rounded to next integer:  [[2007 2048]
 [1630 1638]]
Max value in slity array (ignoring NANs):  0.49934753059464704
percentage of F/O trace that was flagged: 100.0

Working with slit/slice:  4
Slit min and max in y direction:  -0.5 0.5
bounding box rounded to next integer:  [[2017 2048]
 [1320 1328]]
Max value in slity array (ignoring NANs):  0.4992600265017523
percentage of F/O trace that was flagged: 96.6

Working with slit/slice:  5
Slit min and max in y direction:  -0.5 0.5
bounding box rounded to next integer:  [[1873 2048]
 [1590 1600]]
Max value in slity array (ignoring NANs):  0.49970473402574966
percentage of F/O trace that was flagged: 100.0

Working with slit/slice:  9
Slit min and max in y direction:  -0.5 0.5
bounding box rounded to next integer:  [[1511 1939]
 [1262 1270]]
Max value in slity array (ignoring NANs):  0.47541638939121267
percentage of F/O trace that was flagged: 100.0

Working with slit/slice:  10
Slit min and max in y direction:  -0.5 0.5
bounding box rounded to next integer:  [[1515 1943]
 [1230 1240]]
Max value in slity array (ignoring NANs):  0.4999677623917731
percentage of F/O trace that was flagged: 100.0


# Quickly see if the test passed: Do the NIRSpec implementation and the pipeline's agree within <= 99.5%?

print('These are the final results of the tests: ')
for key, val in results_dict.items():
    if not isinstance(val, str):
        if val:
            val = 'PASSED'
        else:
            val = 'FAILED'
    print('{:<40} {:<8}'.format(key, val))

These are the final results of the tests: 
mos_prism_nrs1_uncal.fits                FAILED  
mos_prism_nrs2_uncal.fits                skipped 
mos_g140m_line1_NRS1_uncal.fits          PASSED  
mos_g140m_line1_NRS2_uncal.fits          PASSED  
ifu_prism_nrs1_uncal.fits                PASSED  
ifu_prism_nrs2_uncal.fits                skipped 
ifu_g395h_f290lp_nrs1_uncal.fits         PASSED  
ifu_g395h_f290lp_nrs2_uncal.fits         PASSED

JWST Pipeline Validation Testing Notebook: spec2, msa_flagging step¶

Table of Contents¶

Imports¶

Test Description¶

Results¶

Calibration WG Requested Algorithm:¶

Defining Terms¶

Run the JWST pipeline and msa_flagging validation tests¶

Testing Data Set¶

¶

About this Notebook¶